High Resolution Mapping and Functional Analysis of the Methylome in Arabidopsis (polyA RNA)

Cytosine DNA methylation is important for transposon silencing and epigenetic regulation of endogenous genes. Using a single-chip tiling microarray with 35 bp resolution, we carried out the first unbiased mapping of DNA methylation in the entire genome of the flowering plant Arabidopsis thaliana.Pericentromeric heterochromatin, repetitive sequences and regions producing small interfering RNAs were heavily methylated. Unexpectedly, over one third of expressed genes contained methylation within transcribed regions, whereas only ~5% of genes contained methylation within promoter regions. Interestingly, genes methylated in transcribed regions were highly expressed and constitutively active, whereas promoter-methylated genes showed a greater degree of tissue-specific expression. Analysis of several DNA methyltransferase mutants revealed widespread epigenetic regulation of protein-coding genes as well as non-coding RNA genes of unknown function. Keywords: whole genome profiling, poly(A)RNA, DNA methylation All plants used in this study are of the Columbia accession. The met1 and drm1 drm2 cmt3 mutants are previously published. The mutant alleles are: met1-3; drm1-2, drm2-2, cmt3-11. To avoid variability caused by inbreeding, all homozygous mutants were from F1 segregating populations. Plants were grown under continuous light. RNA was extracted from 5 weeks old plants using the Plant RNeasy Kit (QIAGEN) according to manufacturer’s instructions. The entire aerial parts of 2–3 plants were pooled for each 3 biological replicate.